Months after Asuna's discussion with her mother, she receives a message from Kurahashi that Yuuki is dying and learns that nothing more could be done. While holding Yuuki's hand, Asuna realizes that Yuuki wanted to return to the virtual world, and Kurahashi allows her to FullDive. At the island where Asuna and Yuuki first met, Yuuki creates a scroll for her Original Sword Skill and passes it to Asuna in hopes that it would protect her. The members of the Sleeping Knights, along with Kirito, Klein, Leafa, Lisbeth, Silica, Sinon, Yui, and numerous other fairies arrive to cheer Yuuki on in her final moments, all having been notified by Asuna so that Yuuki would not have a lonely farewell. Yuuki then tells Asuna how she had always asked herself what her reason was for living if she was destined to die anyway, then says that she had found the reason, as her last moments were truly fulfilling. Before Yuuki's death, Asuna vows to meet her in another world. A week later, at Yuuki's memorial service, Asuna meets with An Shiun, Siune's real-life counterpart, whose condition is improving. They learn from Kazuto and Kurahashi that they were talking about applying the Bidirectional Communication Probe for medical FullDive technology, Yuuki having provided more than enough data for the device. When Asuna is surprised that the Medicuboid designs came from an external helper, Kurahashi states that the helper was a professor named Rinko Koujiro, who previously took care of Akihiko Kayaba during the SAO Incident, thus the Medicuboid designs actually came from Akihiko.
On the day after Asuna's reunion with Yuuki, Asuna takes a Bidirectional Communication Probe to guide Yuuki around the school. Yuuki takes part in the lectures and becomes popular with her classmates. Afterwards, Asuna takes Yuuki to the old Konno residence, which Yuuki reveals is about to be torn down soon, so she wished to see it for one last time. She then admits that by seeing her house she realized how her mother had been surrounding her with her feelings. Asuna tells Yuuki about her relationship with her own mother and asks Yuuki how to be as strong as her. However, Yuuki says that she was not strong, but instead, she did not feel like she had time to waste, so she would always be honest with her feelings. She then recommends Asuna to talk with her mother and share what she felt. Using Yuuki's advice, Asuna asks Kyouko to log into ALO with her so she could show it to her. Kyouko reluctantly accepts and uses Asuna's sub account to log in. At the Forest House, Kyouko is reminded of her parents' home. Asuna then tells her mother about how happy her parents were of her and how they wished to protect their home so Kyouko would have a place to return to. Asuna then reveals that she realized how life was not about just doing things for oneself and how the happiness of others could make one happy as well, thus she desires to remain in her current school where she could support the ones she loved. The next morning, Kyouko tells Asuna that if she planned to support someone, she had to be strong herself, thus she would have to work hard on her grades to get into a university and whether Asuna would have to transfer would depend on her progress. Asuna accepts her mother's proposal before leaving.
Three days later after the incident at the Monument of Swordsmen, Asuna tries asking Siune about Yuuki's behavior. She responds that Yuuki was trying to avoid Asuna for her own sake, then asks Asuna to forget about the Sleeping Knights before logging out. At school, Asuna meets up with Kazuto, who gives her the address to a hospital where a medical FullDive machine, the Medicuboid, was being tested. At the hospital, Asuna meets Doctor Kurahashi, Yuuki's supervisor, who explains the Medicuboid's usage for patients in terminal care. Kurahashi then reveals that Yuuki was suffering from AIDS due to an infection via blood transfusion during complicated labor. After Asuna asks why Yuuki started using the Medicuboid, Kurahashi explains that he had her put in a clean room at his own request so she would not risk further infection, and reveals that Yuuki had been living inside the machine for three years straight, not returning to the real world at all. Asuna then learns about Yuuki's elder twin sister, who passed away the year before, causing her to break down in tears. Seeing this, Yuuki communicates with Asuna via the Medicuboid, asking her to meet at the place where they first met in ALO. Asuna uses the AmuSphere in the next room to log into the game and rushes to Yuuki's location. There, the two talk, during which Yuuki expresses her wish of going to school again.
While Kirito battles the raid party's reinforcements, the Sleeping Knights engage the forces blocking the path to the boss room. However, seeing that their assault was useless due to the guild's healers, Asuna asks Siune to manage the healing herself and uses Flashing Penetrator to break through to the healers while killing the group's leader. After the healers are disposed of, followed by the rest of the players, Asuna and the others enter the boss room. During the boss battle, Asuna deduces the boss's weak point and orders Yuuki to use a Sword Skill. Following Asuna's suggestion to use Tecchi as a stepping stone, Yuuki defeats the boss with her signature Original Sword Skill. With the mission concluded, the group agrees to celebrate at Asuna's in-game home. While conversing about various things, Asuna asks whether she could join the Sleeping Knights and notices the unpleasant reactions of the others. The group then goes to the Monument of Swordsmen, where they take a picture. Afterwards, Yuuki accidentally addresses Asuna as her elder sister. Since Yuuki also did so back in the boss room, Asuna points this out to her and Yuuki unexpectedly starts crying and abruptly logs out.
Yuuki takes Asuna to an inn in Ronbaru and introduces her to the other members of the Sleeping Knights: Jun, Nori, Siune, Talken and Tecchi. Yuuki then reveals that the guild wanted Asuna's help in defeating the next Floor Boss with just one party. Siune explains that the group wanted to defeat the boss in order to etch their names on the Monument of Swordsmen, as they would not be able to adventure together after winter. After some thinking, Asuna agrees to help. Sometime later, while she is walking to the Teleport Gate plaza, Kyouko disconnects Asuna from the game and they have a disagreement. Asuna decides to go to a park in another residential area and considers calling Kazuto, but decides that she did not want to expose her weakness to him. The next day, she meets up with the Sleeping Knights and they easily manage to reach the boss room, but Asuna detects several other players hiding near there. Though the players claim they are waiting for their friends, Asuna realizes they were actually spying on their battle to study the boss without sacrificing their own men. After the Sleeping Knights and Asuna are defeated and re-spawn in Ronbaru, Asuna tells the others what she discovered and they decide to rush to the boss room again before the guild had enough time to gather a raid group. At the boss room, they find a large amount of players gathered at the door. As the guild rejects the request of the Sleeping Knights to let them try again, Yuuki declares that they would fight it out and attacks the raid group's leader. At that point, the rest of the raid party arrives, but Kirito appears, having followed them, and blocks their path.
After agreeing to meet everyone the next day, Asuna logs out of ALO to have dinner with her mother Kyouko. Dissatisfied with her daughter being a gamer, Kyouko has hired a personal tutor for Asuna so she could speed up her education, and that she was given an application for an oriented high school that would be able to efficiently teach her for her to go to college at a faster rate. Asuna also realizes that Kyouko investigated Kazuto, whom she objects to their relationship. Asuna abruptly leaves, but not before insulting her mother. In her room, Asuna laments about how she wanted to stay by Kazuto's side and the fact that, while she may have been powerful in SAO, she was powerless in the real world. The next day, Asuna meets with Kirito on the 24th Floor of New Aincrad, and Kirito shares his impressions of Absolute Sword. Leafa, Lisbeth, and Silica then arrive and remind them that Asuna had a duel to get to. At the island, Asuna discovers that Absolute Sword was actually a girl named Yuuki. Asuna challenges Yuuki and finds out how skillful she is. During the duel, Asuna tries activating a rapier Sword Skill, Quadruple Pain, but Yuuki manages to block her attacks and then activates her own Sword Skill. Suffering heavy blows, Asuna activates her Original Sword Skill, Starry Tear. However, while she had used up her last attack, Yuuki's Sword Skill is continuous. However, before she could defeat Asuna, Yuuki stops her assault, then states that she was satisfied with the duel. Yuuki then takes Asuna to Aincrad, where she asks for her help.
During a date at Andrew's (Agil) cafe, Kazuto and Asuna start talking about their old home in Aincrad. Andrew tells them about the revealed contents of the upcoming ALO update, including the introduction of the 21st-30th floors of New Aincrad. On Christmas Eve, when the update takes place, the group challenges the 21st Floor Boss, and after a fierce battle, the group manages to reach the 22nd Floor, and Kirito and Asuna purchase their old home again. Later on, as the group does homework at the house, Lisbeth asks Asuna if she heard about stories about Absolute Sword, an unbeatable player who had likely converted his or her avatar from another game and was challenging other players at an island on the 24th Floor. As Asuna was away during the New Year and did not have access to the Internet, she is unaware of the story. The group decides to challenge Absolute Sword, but Leafa and Lisbeth are all beaten easily. Silica notes that players would likely continue to challenge the mysterious player as they are betting a powerful 11-hit Original Sword Skill. Kirito also fights Absolute Sword and loses. Asuna decides to challenge the player herself, but at that moment, she notices that it is already past her dinnertime. Before she logs out, she asks Lisbeth if Absolute Sword could be an SAO survivor. Lisbeth replies that she asked Kirito what he thought about Absolute Sword after battling him or her; he replied that the player could not have been an SAO survivor, as his Dual Blades skill would have been given to him or her instead of him.
Thrym engages the group in battle, and they are supported by Freyja, who overwhelms Thrym with her own attacks. Thrym retaliates by freezing most of the group with an ice breath, then sending them flying backward with a powerful stomp of his foot. Just as he is about to finish them off, the uninjured Sinon distracts Thrym while the other search for a large golden hammer purported by Freyja to belong to her family, which is essential in defeating him. Kirito finds the hammer and throws it to Freyja, who catches it and then suddenly transforms into Thor, the Norse god of thunder, to everyone's shock. Thor, enraged at Thrym for stealing his hammer, then joins the group in the fight against Thrym. Eventually, they manage to overwhelm him before Thor finishes him off. As a reward for aiding him in Thrym's defeat, Thor grants Klein with Mjölnir, much to his dissatisfaction. A secret staircase then opens up, which leads the group to the bottom of Þrymheimr, and Excaliber. Kirito manages to pull it out of the frozen puddle, but it causes Þrymheimr to fall apart. As the floor they are on plunges down a chasm, they are saved by Tonkii, and Kirito, knowing that Excaliber is too heavy for him to jump onto Tonkii with, throws it down the chasm, but Sinon retrieves it with a magic-assisted arrow. She gives Excaliber back to Kirito under the condition that he remember her every time he uses the sword earning jealous and angry looks for every one. The group then observes as the chasm is flooded with water and the World Tree's roots extend to its surface, causing new trees to grow. Urðr and her sisters Verdandi and Skuld appear and thank them for saving Jötunheimr, and Urðr gifts Kirito with Excaliber. Sometime later, in the real world, Kazuto, Suguha, and Shino test out a device that converts real-time footage into pseudo-3D for Yui to interact in before having lunch with the rest of the group, celebrating the conclusion of the quest.
At the entrance to Thrymheim, Yui explains that the quest the group was given was created by the Cardinal System's Automatic Quest Generation Function and that if they do not succeed in their quest, a final war event, Ragnarok, will be triggered and the world of ALO will be subsequently destroyed, something the Cardinal System is capable of doing. Because they had worked so hard to develop their avatars, the group becomes more determined to finish the quest. At the end of the second floor of Thrymheimr, the group encounters two minotaurs, and they are forced to rely on Sword Skills that could deal elemental damage to them in addition to physical damage, but also leave the player rigid for a few seconds after the skill is used up. With Kirito revealing his new technique of using consecutive Sword Skills with each of his swords to avoid the period of rigidity, they are able to defeat the two minotaurs. Later, after defeating the boss guarding the entrance to the lowest floor of the castle, they encounter a female NPC trapped in an ice cage along the way. Although the others insist that it is a trap and plan to avoid her, Klein, captivated by the woman's beauty, ignores their advice and frees the woman, who introduces herself as Freyja. Instead of running away, Freyja asks to join the group and Kirito reluctantly agrees to the request. After preparing for the final battle by recharging their buffs, the group enters the throne room, where they are met by the massive king of the frost giants, Thrym.
One day at the end of the year, Suguha shows Kazuto a news article about the legendary item, the Holy Sword Excaliber, being discovered in ALO. They then call Asuna, Klein, Lisbeth, Silica, and Sinon to challenge the dungeon in the sky of Jötunheimr, where Excaliber was located. After preparing their items at Lisbeth's arms shop and purchasing potions for the adventure, the group enters Jötunheimr via a secret passageway in Alne. At the end of the tunnel, they reach the top of Jötunheimr and Leafa calls Tonkii, a flying evil-god-class monster that they had befriended several months ago. The group climbs on Tonkii's back and asks it to take them to the dungeon. However, along the way, Tonkii suddenly dives downward and stops at an altitude where they could see the ground. There, they see that players were cooperating with the humanoid evil-god-class monsters to massacre Tonkii's kin, the beast evil-god-class monsters. As they watch the scene, a giant NPC, the Queen of the Lake Urðr, appears behind them. She explains that the massacre was ordered by the king of the giants, Þrym, who once threw the Holy Sword Excaliber into Urðr's Spring and caused the world of Jötunheimr to turn into an icy wasteland. She then states that if all of Tonkii's kin are slaughtered, she would lose her power and this would allow Þrym to invade Alfheim. To prevent this, Urðr requests the fairies to retrieve the Holy Sword Excaliber from the bottom of the ice dungeon, called Þrymheimr.